I solved the problem and thought I'd pass it along.  The BIOS also has a SATA AHCI setting which was disabled.  After I enabled it, the disks are now recognized as /dev/sd? and I'm getting more reasonable disk speeds.  I also do not get the ata_piix message about "no available legacy ports".

Ken

Ken Teh wrote:
> I just installed SL5.3 on a Supermicro PDSBE motherboard and its disk 
> i/o is painfully slow; about 3MB/s.  The system has SATA drives but the 
> kernel sees them as /dev/hdx devices.  There is also a ata_piix message 
> at the beginning of bootup that says "no available legacy port".  I'm 
> guessing the failure to recognize the SATA drives as /dev/sdx and the 
> slow disk i/o are related to this cryptic message.
> 
> I ran a Fedora 11 live CD on the system and it can do disk i/o easily 
> 20-30 times faster which is closer to what I expect.  100MB/s or more.  
> I'm pretty sure the problem is kernel related.
> 
> I tried switching the SATA mode in the BIOS to compability instead of 
> enhanced.  It didn't make any difference.  I wasn't expecting any.  The 
> compatibility vs native stuff, I thought, was something that was done 
> when SATA support for spotty.  The SATA controller is an Intel ICH8 
> which I figure should be well supported.
> 
> I also looked at the dumps of hdparm both under SL53 and Fedora 11.  The 
> features enabled are the same for both.  There are additional features 
> listed under Fedora 11, all SCT (SMART Command Transport) related.  
> There is also a whole bunch of dma modes displayed in both hdparm -t 
> dumps.  On SL53 there is a * next to udma5 while it's next to udma6 
> under Fedora.  I'm not sure what this means.
> 
> Any ideas on how to proceed?  Build a custom kernel?  Which I am 
> reluctant to do since I rely on SL for updates.
> 
> Ken